LDO

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Viewing 9 posts - 1 through 9 (of 9 total)
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  • in reply to: Interruption with command line tools #1923
    LDO
    Participant

    Thank you for this. Unfortunately that was from 4 or 5 months ago and I no longer remember which image that was.

    in reply to: svreg command line "cores" #1845
    LDO
    Participant

    Of course this is done after having run the Cortical Extraction Sequence first.
    Then, here is a bit of the Matlab code used to call svreg:

    Name = ’xnrT1.nii.gz’ %(skull stripped T1)
    basename = string(name(1:(length(name)-7))) %(.nii.gz extension)
    st=’svreg.exe ‘+ basename + ‘ -U’
    dos(st)

    This results in:
    basename= ‘xnrT1’
    st=svreg.exe “C:\Users\Larry Olson\Desktop\jtTestCase\BS”\xnrT1 -U
    these are the errors (from running the script OR from pasting into matlab command window):
    …curvature resolution 8/10
    curvature resolution 9/10
    curvature resolution 10/10
    Multiresolution curvature maps are calculated
    Computing additive curvature
    Performing curvature registration
    Curvature registration at resolution 1/4
    Error using imhist (line 76)
    Invalid MEX-file ‘C:\Users\LARRYO~1\AppData\Local\Temp\Larry Olson\mcrCache9.0\svreg_1\toolbox\images\images\private\imhistc.mexw64’: The specified procedure could not be found.
    Error in histeq>computeCumulativeHistogram (line 181)
    Error in histeq (line 138)
    Error in register_images_elastic_anand_landmarks_cg (line 26)
    Error in curvature_registration512g_wt_multi_bs_elastic_xyz_cg (line 129)
    Error in curvature_registration_newbs_elastic_xyz (line 73)
    Error in svreg_label_surf_hemi (line 191)
    Error in svreg (line 180)
    MATLAB:invalidMEXFile
    ans =
    -1

    Note I pasted the exact same call into a DOS Command Prompt, and it ran all the way through:
    svreg.exe “C:\Users\Larry Olson\Desktop\jtTestCase\BS”\xnrT1 –U

    Had to use the –U flag because this machine is only a dual core i5

    in reply to: svreg command line "cores" #1843
    LDO
    Participant

    “check environment variables in matlab by typing env”
    >’env’ is not recognized as an internal or external command, operable program or batch file.
    (On Windows here)

    Actually I have only one Matlab Compiler Runtime: 7.13
    But 3 Matlab Runtimes: 9.0, 9.5, 9.6

    Not sure how to check environment variables…

    in reply to: svreg command line "cores" #1841
    LDO
    Participant

    No, it is 64 bit MCR
    It works from the GUI
    It works (with the same DOS command) from the Windows command prompt
    *It just aborts part way through (with the same DOS command) when started within Matlab

    (MCR_R2015b_win64_installer.exe)
    (but I also have other versions installed for creating Matlab standalone programs)

    That is so puzzling

    in reply to: svreg command line "cores" #1839
    LDO
    Participant

    See above. The svreg.exe with -U failed when I called it from Matlab 2019a. I just ran exactly the same call from the command prompt in Windows and it worked perfectly. I am puzzled…

    in reply to: svreg command line "cores" #1838
    LDO
    Participant

    Yes! That did start the process.
    But it stops after a few minutes:

    …curvature resolution 10/10
    Multiresolution curvature maps are calculated
    Computing additive curvature
    Performing curvature registration
    Curvature registration at resolution 1/4
    Error using imhist (line 76)
    Invalid MEX-file ‘C:\Users\LARRYO~1\AppData\Local\Temp\Larry Olson\mcrCache9.0\svreg_0\toolbox\images\images\private\imhistc.mexw64’: The specified procedure could not be found.

    Error in histeq>computeCumulativeHistogram (line 181)
    Error in histeq (line 138)
    Error in register_images_elastic_anand_landmarks_cg (line 26)
    Error in curvature_registration512g_wt_multi_bs_elastic_xyz_cg (line 129)
    Error in curvature_registration_newbs_elastic_xyz (line 73)
    Error in svreg_label_surf_hemi (line 165)
    Error in svreg (line 180)
    MATLAB:invalidMEXFile

    But, oddly, if I look in ‘C:\Users\LARRYO~1\AppData\Local\Temp\Larry Olson\mcrCache9.0\svreg_0\toolbox\images\images\private\imhistc.mexw64’, imhistc.mexw64 is there

    in reply to: svreg warp #1568
    LDO
    Participant

    Yes, this file exists: C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT.svreg.init.label.nii.gz as C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT1.svreg.init.label.nii but has been converted to uncompressed nifty for compatibility with Matlab SPM tools.

    Is that really a problem?

    in reply to: svreg warp #1565
    LDO
    Participant

    Joshi,

    ———————————————————————————————
    FYI, I sent email to your response but got this:
    ” —– The following addresses had permanent fatal errors —– <cbhushan@usc.edu>
    (reason: 550-5.2.1 The email account that you tried to reach is disabled. Learn more at)”
    ———————————————————————————————

    Thank you for your prompt response! Difficult to troubleshoot, but I get this error:

    C:\Program Files\BrainSuite18a\svreg\bin>svreg_labelwith_atlas.exe C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT1 C:\Users\lolson\Desktop\BrainSuiteAtlas1\mri mod
    Error using copyfile
    No matching files were found.

    Error in svreg_labelwith_atlas (line 77)

    MATLAB:COPYFILE:FileDoesNotExist

    Not sure which files are missing?
    Thanks

    in reply to: Output header error #1159
    LDO
    Participant

    Same issue with files saved by version 18a

Viewing 9 posts - 1 through 9 (of 9 total)